arXiv subjects

Anna Giannakou

Publications and source records attributed to Anna Giannakou.

3 recordsLinked to original sources

arXiv2026

Toward Trustworthy Autonomous Science: A Two-Year Community Roadmap

One year ago, the AISLE roadmap argued that autonomous laboratories operated as isolated islands and proposed a grassroots network organized around five critical dimensions. The field has since moved faster than anticipated. Multi-agent systems have produced experimentally validated hypotheses, self-driving laboratories have grown more interoperable and orchestrated, reasoning-trained and domain foundation models have raised the capability ceiling, and the Genesis Mission has placed autonomous experimentation at the center of U.S. federal science strategy, with industry emerging as a primary actor. Progress has met a sobering counter-current, including a corrected flagship discovery result, benchmarks showing that agents which rival experts on closed-ended questions still complete only a fraction of open-ended research, and fabricated citations surfacing at leading venues. We read this as the defining tension of the field. Producing a candidate discovery is no longer the hard part, but verifying it is, and this asymmetry now limits autonomous science more than raw model capability. We update the roadmap around seven dimensions, revisiting the original five and elevating two former cross-cutting concerns, trust, verification, and reproducibility, and safety, security, and governance, to first-class status. We assess the original milestones (M1 through M14) as achieved, partially achieved, reframed, or open, add four new milestones (M15 through M18), and scope the path forward to a two-year horizon. The first year concentrates on interfaces, protocol adoption, and the scaffolding of verification, and the second targets federation, zero-trust coordination, and governance. Throughout, we position the grassroots network as the interoperability fabric that lets national programs, international initiatives, and commercial platforms connect rather than re-silo.

cs.DC↗

arXiv2023

Automated Annotation of Scientific Texts for ML-based Keyphrase Extraction and Validation

Advanced omics technologies and facilities generate a wealth of valuable data daily; however, the data often lacks the essential metadata required for researchers to find and search them effectively. The lack of metadata poses a significant challenge in the utilization of these datasets. Machine learning-based metadata extraction techniques have emerged as a potentially viable approach to automatically annotating scientific datasets with the metadata necessary for enabling effective search. Text labeling, usually performed manually, plays a crucial role in validating machine-extracted metadata. However, manual labeling is time-consuming; thus, there is an need to develop automated text labeling techniques in order to accelerate the process of scientific innovation. This need is particularly urgent in fields such as environmental genomics and microbiome science, which have historically received less attention in terms of metadata curation and creation of gold-standard text mining datasets. In this paper, we present two novel automated text labeling approaches for the validation of ML-generated metadata for unlabeled texts, with specific applications in environmental genomics. Our techniques show the potential of two new ways to leverage existing information about the unlabeled texts and the scientific domain. The first technique exploits relationships between different types of data sources related to the same research study, such as publications and proposals. The second technique takes advantage of domain-specific controlled vocabularies or ontologies. In this paper, we detail applying these approaches for ML-generated metadata validation. Our results show that the proposed label assignment approaches can generate both generic and highly-specific text labels for the unlabeled texts, with up to 44% of the labels matching with those suggested by a ML keyword extraction algorithm.

cs.IR↗

arXiv2020

Performance Analysis of Scientific Computing Workloads on Trusted Execution Environments

Scientific computing sometimes involves computation on sensitive data. Depending on the data and the execution environment, the HPC (high-performance computing) user or data provider may require confidentiality and/or integrity guarantees. To study the applicability of hardware-based trusted execution environments (TEEs) to enable secure scientific computing, we deeply analyze the performance impact of AMD SEV and Intel SGX for diverse HPC benchmarks including traditional scientific computing, machine learning, graph analytics, and emerging scientific computing workloads. We observe three main findings: 1) SEV requires careful memory placement on large scale NUMA machines (1$\times$$-$3.4$\times$ slowdown without and 1$\times$$-$1.15$\times$ slowdown with NUMA aware placement), 2) virtualization$-$a prerequisite for SEV$-$results in performance degradation for workloads with irregular memory accesses and large working sets (1$\times$$-$4$\times$ slowdown compared to native execution for graph applications) and 3) SGX is inappropriate for HPC given its limited secure memory size and inflexible programming model (1.2$\times$$-$126$\times$ slowdown over unsecure execution). Finally, we discuss forthcoming new TEE designs and their potential impact on scientific computing.

cs.DC↗